Research workbench
Cryo-EM structure of bsclpp-ADEP1 complex at pH 4.2
Analyse Cryo-EM structure of bsclpp-ADEP1 complex at pH 4.2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FER
- Type
- protein
- Length
- 2,436 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; ADEP1
- EC
- 3.4.21.92
- UniProt
- P80244
- Ligands
- OTT
- Pockets
- 20 · best druggability 0.63
Structure
electron microscopy · 2 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 168 | 40% helix, 13% strand | P80244 |
| O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b | ADEP1 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- OTT · (2E,4E,6E)-octa-2,4,6-trienoic acid · ligand · 14 copies · chains A, G, O, B, P, C, Q, D, R, E, S, F, T, U, H, V, I, W, J, X, K, Y, L, Z, M, a, N, b
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.63 | 0.76 | 51 | empty |
| 2 | 522 | 0.63 | 0.75 | 55 | empty |
| 3 | 319 | 0.56 | 0.76 | 39 | empty |
| 4 | 166 | 0.56 | 0.80 | 25 | OTT |
| 5 | 154 | 0.55 | 0.81 | 26 | OTT |
Interfaces
56 interfaces between chains.
- A–B · 911 Ų buried · 4 hydrogen bonds · protein-protein
- K–L · 896 Ų buried · 3 hydrogen bonds · protein-protein
- M–N · 895 Ų buried · 3 hydrogen bonds · protein-protein
- F–G · 890 Ų buried · 3 hydrogen bonds · protein-protein
- A–G · 890 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 14 covalent (nonstandard, covalent ligand).
Compared structures
- 7FER · Cryo-EM structure of BsClpP-ADEP1 complex at pH 4.2 · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P80244
- Elsewhere: RCSB PDB 7FER · PDBe 7FER · UniProt P80244
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